Bowtie2 code help

Question

[sghoshucla]

Hi I am new to RNA seq analysis. I am trying to run bowtie2 in command line but failed. can somebody help with the code

qsub -l h_data=4G,time=2:00:00 -cwd -b y ‘module load bowtie2; bowtie2 -p 4 -x Bowtie2Index -1N704.fastq -S bowtie.N704’

also I would like to know if I can get a separate file for unaligned reads.

thanks

[Devon Ryan]

Try -U rather than -1 and make sure it has a space after it. Also, if a command "fails", it helps if you describe in what way it fails and whether you get an error message...

[sghoshucla]

Thanks Eagle Eye and Devon Ryan. I have one more question. I am analyzing samples from yeast. should I use jut BowtieIndex or something else? also, I would like to know whether I can get the reads that are not aligned.

thanks

[GenoMax]

Use bowtie2index for yeast genome.
Check the --un and --un-conc options for bowtie2. That should allow you to collect reads that don't align into a file.

Answer 1

[EagleEye]

If you say RNAseq analysis, bowtie is not a good idea. Use some splice aware aligner like Tophat, STAR, GSNAP or SOAP-splice.

Answer to the command: try with -U

bowtie2 -p 4 -x Bowtie2Index -U N704.fastq -S bowtie.N704